debian/bin/spades

 #!/bin/sh
 SPADESDIR=/usr/lib/spades/bin
-# SPADESSHARE=/usr/share/spades
+SPADESSHARE=/usr/share/spades
 exename=`basename $0`
 PATH=$SPADESDIR:$PATH
 if [ -f $SPADESDIR/${exename}.py ]; then

debian/links

@@ -10,7 +10,7 @@ usr/bin/spades  usr/bin/plasmidspades.py
 usr/bin/spades  usr/bin/plasmidspades
 usr/bin/spades  usr/bin/rnaspades.py
 usr/bin/spades  usr/bin/rnaspades
-usr/bin/bwa     usr/lib/spades/bin/bwa-spades
+usr/bin/bwa     usr/lib/spades/bin/spades-bwa
 usr/share/man/man1/spades.1.gz /usr/share/man/man1/spades.py.1.gz
 usr/share/man/man1/dipspades.1.gz /usr/share/man/man1/dipspades.py.1.gz
 usr/share/man/man1/truspades.1.gz /usr/share/man/man1/truspades.py.1.gz

debian/patches/0118_adjust_spades_home_again.patch

+--- spades.orig/spades_init.py
++++ spades/spades_init.py
+@@ -32,7 +32,7 @@
+     if isfile(os.path.join(spades_home, 'spades-core')):
+         install_prefix = dirname(spades_home)
+         bin_home = join(install_prefix, 'bin')
+-        spades_home = join(install_prefix, 'share', 'spades')
++        spades_home = join(install_prefix, '../../', 'share', 'spades')
+         python_modules_home = spades_home
+         ext_python_modules_home = spades_home
+ 

debian/patches/series

+0118_adjust_spades_home_again.patch
 0002_use_debian_packaged_python-joblib.patch
 0003_accept-system-bwa.patch
 0101_cmake_ignore_removed_python-yaml.patch
@@ -10,7 +11,6 @@
 # use-debian-packaged-bamtools.patch   ## <<-- does not work - see patch description
 # use-debian-packaged-yaml-cpp.patch   ## <<-- does not work - see patch description
 0110_build_single_thread.patch
-0113_adjust_paths.patch
 0114_use_debian_provided_libs.patch
 0115_enable_compiler_messages.patch
 0111_use_full_config_dirs.patch

debian/rules

@@ -54,6 +54,10 @@ override_dh_installman:
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	# Ugly hack to make files available for dh_aut_test and autopkgtest
+	mkdir -p $(CURDIR)/../share/
+	ln -s $(CURDIR)/install_spades/share/spades $(CURDIR)/../share/
+	ln -s  /usr/bin/bwa $(CURDIR)/install_spades/bin/spades-bwa
 	$(TMPDIR)/bin/spades.py --test
 	$(TMPDIR)/bin/dipspades.py --test
 	$(TMPDIR)/bin/metaspades.py --test
@@ -62,10 +66,14 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	# is still not in the right place. Let's do this later in an
 	# autopkgtest.
 	# $(TMPDIR)/bin/truspades.py --test
+	# Cleunup symlinks
+	rm -rf $(CURDIR)/../share/
+	unlink $(CURDIR)/install_spades/bin/spades-bwa
 endif
 
 override_dh_auto_install:
 	echo "Nothing to install"
+	find $(CURDIR) -name *.pyc -delete
 
 override_dh_install:
 	dh_install
@@ -76,6 +84,7 @@ override_dh_install:
 	chmod +x debian/$(DEB_SOURCE)/usr/bin/spades
 	rm -f debian/$(DEB_SOURCE)/usr/share/spades/GPLv2.txt
 	rm -f debian/$(DEB_SOURCE)/usr/share/spades/LICENSE
+	ln -s ../../../share/spades/VERSION debian/$(DEB_SOURCE)/usr/lib/spades/bin/VERSION
 
 override_dh_installdocs:
 	dh_installdocs

debian/tests/control

 Tests: run-upstreams-tests
-Depends: @
+Depends: @,bwa
 Restrictions: allow-stderr